Microsatellite genetic markers are becoming increasing important tools in the investigation of alternate reproductive strategies in wild plants and animals, and in the implementation of optimal breeding programs for endangered species, and managed cultured populations. Overall, little attention is paid to the frequency and impact of scoring errors and mutations on the resolution and accuracy of such analyses. Here, parentage of 792 Atlantic salmon (Salmo salar) reared communally were determined using di- and tetranucleotide microsatellites. Over 99·5% of the offspring could be unambiguously matched to one set of parents in the original 12 (1 × 1) experimental cross (each of 12 males uniquely crossed to one of 12 females) and in a simulated 36 (1 × 1) cross (involving additional parents), and over 80% in a 12 × 12 cross (all 12 males crossed to all 12 females). Mutations were rare (≈3·4 × 10−−4), though scoring errors were relatively common (2–3% per allele scored), with the rate of error varying among loci. Approximately 90% of scoring errors (or mutations) are expected to be detected in this analysis, and of those that are not, fewer than 0·5% should lead to a false or incorrect determinations of parentage. Based on several indices, we expect that greater than 99·7% of offspring assayed were matched to their true parents.